Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate PfGW456L13_3604 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3604 Length = 490 Score = 319 bits (818), Expect = 1e-91 Identities = 188/476 (39%), Positives = 270/476 (56%), Gaps = 9/476 (1%) Query: 13 FINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEA-KTAWRKLTGAE 71 +INGEWV G + V +PA V T EDV+ AV AA A W + +GAE Sbjct: 6 YINGEWVSPDLGGYLDVIDPA-TEQAFHRVAAGTEEDVDHAVRAARRAFDNGWGQTSGAE 64 Query: 72 RGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGDVI 131 RGQ+L AD +E + +A R+ GK LPEA+ + IA RYYAG Sbjct: 65 RGQWLEALADELESGQQALAELEVRDNGKPLPEAQWDIGDAIACFRYYAGLARELDQQQD 124 Query: 132 PSTDKDALMFTTRV---PLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188 F R+ P+GV G I PWN+P+ + WK+APAL G TVV+KP+ T +T Sbjct: 125 QPLALPDARFCCRIRHEPIGVAGQIIPWNYPLLMAAWKVAPALAAGATVVLKPSELTPLT 184 Query: 189 CAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALAR 248 ++ A + GLPAGV+NLVTG G+ G L EH GV+ + FTGS G I AA Sbjct: 185 ALELAAAADRIGLPAGVLNLVTGLGADAGSPLTEHPGVDKLAFTGSVPTGAKIMSAAARD 244 Query: 249 GAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEK 308 LE+GGK+ IV DDAD+EAA E ++ G F + GQ C+ATSR++VQ I R E+ Sbjct: 245 IKNISLELGGKSAFIVFDDADVEAAVEWILFGIFWNQGQVCSATSRLLVQETIAARLIER 304 Query: 309 LLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQN 368 L++ T+ I+IG ++ V +GP+ S+ Q D L +I++G GA LL GG + + Sbjct: 305 LVEETRKISIGPGMQPGVLLGPLVSQGQYDKVLGFIDQGLASGARLLTGGRR--PAHLRE 362 Query: 369 GYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIG 428 GY+V+PAIFD + +EE+FGPV+ + + + E+AL +AN +FGL+A++ + ++ Sbjct: 363 GYFVEPAIFDEPGHSSILWREEVFGPVLCIKRFKTEEQALQMANASRFGLAAAVMSADLQ 422 Query: 429 RMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTV 484 R +++ AG+V +N S ++AP+GGMK S RE G+ + +K V Sbjct: 423 RTARVANQLRAGIVWVNC-SQPTFVEAPWGGMKHSGI-GRELGQWGLHNYLEVKQV 476 Lambda K H 0.315 0.132 0.374 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 569 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 488 Length of database: 490 Length adjustment: 34 Effective length of query: 454 Effective length of database: 456 Effective search space: 207024 Effective search space used: 207024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory